Pseudomonas aeruginosa is a versatile Gram-negative bacterium that is able to adapt to and thrive in many ecological niches, from water and soil to plant and animal tissues. The bacterium is capable of utilizing a wide range of organic compounds as food sources, thus giving it an exceptional ability to colonize ecological niches where nutrients are limited, such as soil, marshes and coastal marine habitats. Hardalo, C. & Edberg, S. C. Pseudomonas aeruginosa: assessment of risk from drinking water. Crit. Rev. Microbiol. 23,47-75 (1997). It also forms biofilms on wet surfaces such as those of rocks and soil. Costerton, J. W., Stewart, P. S. & Greenberg, E. P. Bacterial biofilms: a common cause of persistent infections. Science 284,13181322 (1999).Aheam, D. G., Borazjani, R. N., Simmons, R. B. & Gabriel, M. M. Primary adhesion of Pseudomonas aeruginosa to inanimate surfaces including biomaterials. Methods Enzymol. 310, 551-557 (1999). Analysis of the P. aeruginosa genome has identified genes involved in locomotion, attachment, transport and utilization of nutrients, antibiotic efflux, and two component and other regulatory systems involved in sensing and responding to environmental changes. Because its natural habitat is the soil, where it exposed to bacilli, actinomycetes and molds, it has developed resistance to a variety of their naturally-occurring antibiotics.
The emergence of P. aeruginosa as a major opportunistic human pathogen during the past century may be a consequence of its resistance to the antibiotics and disinfectants that eliminate other environmental bacteria. P. aeruginosa is now a significant source of bacteraemia in burn victims, urinary-tract infections in catheterized patients, and hospital-acquired pneumonia in patients on respirators. Bodey, G. P., Bolivar, R., Fainstein, V. & Jadeja, L. Infections caused by Pseudomonas aeruginosa. Rev. Infect. Dis. 5, 279-313 (1983). It is also the predominant cause of morbidity and mortality in cystic fibrosis patients, whose abnormal airway epithelia allow long-term colonization of the lungs by P. aeruginosa. Thus, people with cystic fibrosis, burn victims, individuals with cancer and AIDS, and patients requiring extensive stays in intensive care units are particularly at risk of disease resulting from P. aeruginosa infection. P. aeruginosa is also a cause of a variety of different disorders including septicemia, urinary tract infections, pneumonia and chronic lung infections, endocarditis, dermatitis, osteochondritis, ear and eye infections, bone and joint infections, gastrointestinal infections and skin and soft tissue infections, including wound infections, pyoderma and dermatitis.
Cystic fibrosis is one of the most common fatal genetic disorders in the United States, affecting about 30,000 individuals. A comparable number of people in Europe also have CF. It is most prevalent in the Caucasian population, occurring in one of every 3,300 live births. The gene involved in cystic fibrosis was identified in 1989 and codes for a protein called the cystic fibrosis transmembrane conductance regulator (CFTR). This protein, normally produced in a number of tissues throughout the body, regulates the movement of salt and water in and out of these cells. One hallmark of CF is the presence of a thick mucus secretion that clogs the bronchial tubes in the lungs and plugs the exit passages from pancreas and intestines, leading to loss of function of these organs and resulting in a predisposition toward chronic bacterial infections. Pseudomonas aeruginosa, having a propensity to live in warm, wet environments, is a particular problem for CF patients, whose lungs typically become colonized (inhabited long-term) by P. aeruginosa before their 10th birthday. Although antibiotics can decrease the frequency and duration of these attacks, resistant bacteria are quick to develop and the bacteria are never completely eradicated from the lung. More effective antibiotics are necessary for improving lung function and quality of life for CF patients for extended time periods.
Pseudomonas aeruginosa is notorious for its resistance to antibiotics and is, therefore, a particularly dangerous and dreaded pathogen. Todor, K. 2000 Pseudomonas aeruginosa, University of Wisconsin-Madison, available on Apr. 25, 2001 at the URL address: http file type, www host server, domain name bact.wisc.edu, microtextbook/disease directory. The permeability barrier afforded by its outer membrane LPS also contributes to its natural antibiotic resistance, as do the presence of two antibiotic resistance plasmids, both R-factors and RTFs, which are commonly transferred between cells by the bacterial processes of transduction and conjugation. Only a few antibiotics are effective against Pseudomonas, including tobramyocin (TOBI; Chiron), fluoroquinolone, gentamicin and imipenem, and even these antibiotics are not effective against all strains.
Pseudomonas aeruginosa disease generally begins with some alteration or circumvention of normal host defenses and may involve several different virulence determinants. Todor, 2000, supra. The ultimate Pseudomonas infection may be seen as composed of three distinct stages: (1) bacterial attachment and colonization; (2) local invasion; (3) disseminated systemic disease. Particular bacterial determinants of virulence mediate each of these stages and are ultimately responsible for the characteristic syndromes that accompany the disease. For instance, Pseudomonas utilize fimbriae or pili to adhere to the epithelial cells, apparently via binding to specific galactose or mannose or sialic acid receptors on epithelial cells. Fimbrial adherence may be an important step in Pseudomonas keratitis and urinary tract infections, as well as infections of the respiratory tract. Mucoid strains, which produce an a exopolysaccharide (alginate) have an additional or alternative adhesin which attaches to the tracheobronchial mucin (N-acetylglucosamine). Therefore, mucoid strains of P. aeruginosa are commonly seen in lung infections.
The ability of P. aeruginosa to invade tissues depends upon its resistance to phagocytosis and the host immune defenses, and the extracellular enzymes-and toxins that break down physical barriers and otherwise contribute to bacterial invasion. Todor, 2000, supra. For instance, Pseudomonas elastase cleaves collagen, IgG, IgA, and complement, and also lyses fibronectin to expose receptors for bacterial attachment on the mucosa of the lung. Alkaline protease interferes with fibrin formation and lyses fibrin. Together, elastase and alkaline protease destroy the ground substance of the cornea and other supporting structures composed of fibrin and elastin. Elastase and alkaline protease together are also reported to cause the inactivation of ganmna Interferon (IFN) and Tumior Necrosis Factor (TNF).
P. aeruginosa produces three other soluble proteins involved in invasion, including a cytotoxin (MW 25,000) and two hemolysins. Todor, 2000, supra. The cytotoxin is a pore-forming protein originally named leukocidin because of its effect on neutrophils, but it appears to be cytotoxic for most eukaryotic cells. Of the two hemolysins, one is a phospholipase and the other is a lecithinase. They appear to act synergistically to break down lipids and lecithin. The cytotoxin and hemolysins contribute to invasion through their cytotoxic effects on eukaryotic cells.
Pseudornonas aeruginosa also produces two extracellular protein toxins, Exoenzyme S and Exotoxin A. Exoenzyme S may act to impair the function of phagocytic cells in the bloodstream and internal organs to prepare for invasion by P. aeruginosa, and is typically produced by bacteria growing in burned tissue. Exotoxin A is partially identical to diphtheria toxin, and exhibits a necrotizing activity at the site of bacterial colonization and is thereby thought to contribute to the colonization process. Indirect evidence involving the role of exotoxin A in disease is seen in the increased chance of survival in patients with Pseudomonas septicemia that is correlated with the titer of anti-exotoxin A antibodies in the serum.
While therapeutic measures aimed at any of the above virulence factors may help to slow the progression of an infection and may be useful in combined therapeutic regimens, given the variety of virulence factors of P. aeruginosa, antibacterial agents that inhibit growing bacteria by interacting with essential genes and essential gene products are necessary. Although, this is not to say that genes encoding virulence factors would not be essential to survival in particular niches or environments, emphasizing the importance of screening for gene essentiality in various pathogenic environments. See, e.g., Coulter et al., 1998, Staphylococcus aureus genetic loci impacting growth and survival in multiple infection environments, Mol. Microbiol. 30(2): 393-404. However, as P. aeruginosa becomes more and more resistant to existing antibacterial agents, new compounds are required.
Indeed, reports of bacterial strains resistant to the most powerful known antibiotics are becoming more common, signaling that new antibiotics are needed for all bacteria, not only P. aeruginosa. For instance, the United States Center for Disease Control recently announced that one of the most powerful known antibiotics, vancomycin, was unable to treat an infection of Staphylococcus aureus (staph), an organism commonly found in the environment and responsible for many nosocomial infections. If this trend continues, some have warned that we could return to a time when a common bacterial infection is a life threatening matter. See Zyskind et al., WO 00/44906, published Aug. 3, 2000.
Historically, however, the identification of new antibacterial drugs has been painstaking and laborious with no guarantee of success. Traditional methods involve blindly and randomly testing potential drug candidate molecules, with the hopes that one might be effective. Today, the average cost to discover and develop a new drug is nearly $500 million, and the average time is 15 years from laboratory to patient. New identification and screening methods that shorten and improve this process are much needed.
A newly emerging technique for identifying new antibacterial agents is to first identify gene sequences and proteins required for the proliferation of bacteria, or “essential” genes and proteins, and then conduct a biochemical and structural analysis of that target gene or protein in order to derive compounds that interact with the target. Such methodology employs molecular modeling techniques, combinatorial chemistry and other means to design candidate drugs, and offers a more directed alternative to merely screening random compounds with the hope that one might be suitable for a particular bacterium.
Nevertheless, even this preferred approach presents obstacles including the identification of essential genes and proteins, and the design of new assays for the genes thus identified in order to efficiently screen candidate compounds. Several groups have proposed systems for the identification of essential genes. For instance, Zyskind and colleagues propose a method of identifying essential genes in Escherichia coli by subcloning a library of E. coli nucleic acid sequences into an inducible expression vector, introducing the vectors into a population of E. coli cells, isolating those vectors that, upon activation and expression, negatively impact the growth of the E. coil cell, and characterizing the nucleic acid sequences and open reading frames contained on the subclones identified. See WO 00/44906, herein incorporated by reference. The disadvantage of this method is that the overexpression of nonessential genes can also negatively impact the cell, particularly the overexpression of membrane proteins and sugar transport proteins that are not necessary for growth where alternative carbon sources exist. Such proteins typically become trapped in membrane export systems when the cell is overloaded, and would be identified by this methodology. See Muller, FEMS Microbiol. Lett. 1999 Jul. 1;176(1):219-27.
Another group proposes the identification of growth conditional mutants, and more specifically temperature sensitive (ts) mutants, as a means to identify essential genes in Staphylococcus aureus. See Benton et al., U.S. Pat. No. 6,037,123, issued Mar. 14, 2000, herein incorporated by reference. Each gene is identified by isolating recombinant bacteria derived from growth conditional mutant strains, i.e., following introduction of a vector containing a library of nucleic acid sequences, which would grow under non-permissive conditions but which were not revertants. These recombinant bacteria were found to contain DNA inserts that encoded wild type gene products that replaced the function of the mutated gene under non-permissive growth conditions. By this method, Benton and colleagues were able to identify 38 loci on the S. aureus chromosome, each consisting of at least one essential gene.
The disadvantages of this method are first, the chemical employed to induce mutagenesis (diethyl sulfate, DES) is capable of causing several mutations in the same cell, thereby complicating interpretation of the results. Second, the method is particularly labor intensive in that one must painstakingly analyze replica plates of individual colonies grown at permissive and non-permissive temperatures, where replica plates include both mutant and non-mutant cells. Thus, employing the appropriate level of mutagen to achieve a balance between minimizing the number of non-mutant colonies one must screen in order to identify one mutant, while at the same time avoiding multiple mutations in the same cell, may be an arduous task.
Another group has proposed a transposon mutagenesis system for identifying essential genes called “GAMBIT” (“genomic analysis and mapping by in vitro transposition”), and has used the system to identify essential genes first in the gram positive bacteria Haemophilus influenzae and Streptococcus pneumoniae, and more recently in Pseudomonas aeruginosa. See Akerley et al., Systematic identification of essential genes by In vitro mariner mutagenesis, Proc. Natl. Acad. Sci USA 95(15): 8927-32; Wong and Mekalanos, 2000, Proc. Natl. Acad. Sci. USA 97(18): 10191-96; and Mekalanos et al., U.S. Pat. No. 6,207,384, issued Mar. 27, 2001, herein incorporated by reference. GAMBIT involves first isolating and purifying specific genomic segments of approximately 10 kilobases using extended-length PCR, and creating a high density transposon insertion map of the isolated region using Himar1 transposon mutagenesis. The transposon insertions are then transferred to the chromosome following transformation of the bacteria with the transposon containing vectors, and selection for the antibiotic resistance marker on the transposon. The position of each transposon insertion with respect to a given PCR primer is then determined by genetic footprinting, i.e., by amplifying sub-PCR products using one of the original PCR primers and a primer that recognizes an internal site in the Himer1 transposon. By analyzing the length of PCR fragments thus identified, it is possible to identify regions that are devoid of transposon insertions, thereby signaling regions that might contain essential genes.
While the GAMBIT method is a good technique for looking at a small region of the genome for essential genes, it would be extremely labor intensive to use this method for analyzing the entire genome. This is particularly true for P. aeruginosa, whose genome (˜6 megabases) is about 70% greater in size than the H. influenzae genome (˜1.8 megabases). Furthermore, GAMBIT would not be readily applicable to use in organisms that are less recombinogenic than H. influenzae. Indeed, while the H. influenzae genome contains about 1700 protein coding genes, P. aeruginosa contains about 5570. According to U.S. Pat. No. 6,207,384, one would need to clone and mutagenize the 6 million base pair genome of P. aeruginosa in 10,000 base pair fragments, isolating and characterizing 400-800 mutants per 10,000 base pair fragment. Generating 6×105 mutants and characterizing them via PCR on gels would require a significant investment of labor, materials and time.
Another group at Abbott Laboratories has proposed a genome scanning method for identification of putative essential genes in H. influeinzae, whereby random transposon insertions are mapped and analyzed to identify open reading frames containing no insertion in order to identify putative essential genes. Reich et al., 1999, Genome Scanning in Haemophilus influenzae for Identification of Essential Genes, J. Bacteriol. 181(16): 4961-68. However, even though transposon insertions were isolated that spanned the whole genome, the authors employed a genomic footprinting technique similar to that used in GAMBIT to map insertions in a short contiguous region of the chromosome. The method further employs the methods of mutation exclusion and zero time analysis in order to monitor the fate of individual insertions after transformation in growing culture, which looks at individual insertions on a case-by-case basis. Again, such techniques would be extremely labor-intensive for the P. aeruginosa genome, which is 70% larger than the genome of H. influenzae. 
Wong and Mekalanos also proposed identifying essential genes in P. aeruginosa by starting with the knowledge of three essential genes in H. influenzae and using genetic footprint analysis to determine if the homologues of these genes are essential in P. aeruginosa. Of three homologues tested, only one was unable to accommodate a transposon insertion. See Wong and Mekalanos, supra. Such results underscore the fact that a gene that is shown to be essential in one species will not necessarily be essential in another, given that some gene products may fulfill different functional roles in different species. Furthermore, given the larger coding capacity of the P. aeruginosa genome relative to that of other bacteria, it would not be surprising for P. aeruginosa to possess an increase in redundant gene functions, thereby decreasing the actual number of essential genes, and making them more difficult to identify.
Another method is entitled Transposon Mediated Differential Hybridisation (TMDH), which is disclosed in WO 01/07651, herein incorporated by reference. This method entails (i) providing a library of transposon mutants of the target organism; (ii) isolating polynucleotide sequences from the library which flank inserted transposons; (iii) hybridising said polynucleotide sequences with a polynucleotide library from said organism; and (iv) identifying a polynucleotide in the polynucleotide library to which said polynucleotide sequences do not hybridise in order to identify an essential gene of the organism. However, the problem with this methodology is that it has a high propensity to lead to false positives, and many essential genes will be missed. Furthermore, the method does not yield any detailed information regarding the loci disrupted by transposons, or whether they were hit more than once.
Thus, there is a great need for more efficient methods to identify essential genes, particularly in P. aeruginosa, so that new antibacterial agents may be designed therefrom for use in treatment of P. aeruginosa infections.